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For hg38
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For hg19
BigWig
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Peak-call (q < 1E-10)
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For hg38
Colocalization
Target Genes (TSS ± 1kb)
Target Genes (TSS ± 5kb)
Target Genes (TSS ± 10kb)
For hg19
Colocalization
Target Genes (TSS ± 1kb)
Target Genes (TSS ± 5kb)
Target Genes (TSS ± 10kb)
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For hg38
BigWig
Peak-call (q < 1E-05)
Peak-call (q < 1E-10)
Peak-call (q < 1E-20)
For hg19
BigWig
Peak-call (q < 1E-05)
Peak-call (q < 1E-10)
Peak-call (q < 1E-20)
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Sequence Read Archive
DBCLS SRA
NCBI SRA
ENA
Antigen: CTCF
wikigenes
PDBj
CellType: SNU-475
ATCC
MeSH
RIKEN BRC
Variation
TogoVar
DRX313746
Illumina NovaSeq 6000 paired end sequencing of SAMD00410987
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
TFs and others
Antigen
CTCF
Cell type
Cell type Class
Liver
Cell type
SNU-475
Primary Tissue
Liver
Tissue Diagnosis
Carcinoma Hepatocellular
Attributes by original data submitter
Sample
sample_name
SNU475_4_Dox_minus_CTCF_r2
antibody
CTCF (Cell Signaling Technology, #3418S, Lot 4)
biological_replicate
2
biomaterial_provider
American Type Culture Collection (ATCC)
cell_line
SNU475
cell_type
hepatocellular carcinoma
culture_collection
ATCC: CRL-2236
dev_stage
adult
disease
hepatocellular carcinoma
genetic_modification
Lentiviral/Retroviral vector-mediated
growth_condition
RPMI-1640 with 10% fetal bovine serum (FBS)
growth_protocol
maintained as adherent cells
sample_type
cultured cells
sex
male
temp
37
Sequenced DNA Library
library_name
475_4_m_CTCF_r2
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
"QIAseq Ultralow Input Library Kit (QIAGEN, #180492)"
Sequencing Platform
instrument_model
Illumina NovaSeq 6000
Where can I get the processing logs?
Read processing pipeline
log
hg38
Number of total reads
59939017
Reads aligned (%)
98.1
Duplicates removed (%)
20.4
Number of peaks
1454 (qval < 1E-05)
hg19
Number of total reads
59939017
Reads aligned (%)
97.2
Duplicates removed (%)
21.1
Number of peaks
1037 (qval < 1E-05)
Base call quality data from
DBCLS SRA